Squashed commit of the following:

commit c031c8b
Author: David Hensle <hensle93@gmail.com>
Date:   Fri Feb 13 15:48:35 2026 -0800

    adding ignore list to skim load for unused skims

commit 83613b2
Author: Copilot <198982749+Copilot@users.noreply.github.com>
Date:   Thu Feb 12 16:30:58 2026 -0600

    Fix Sphinx currentmodule directive for location choice documentation (ActivitySim#1034)

    * Initial plan

    * Fix currentmodule directive in work_location_choice.md and school_location_choice.md

    Co-authored-by: jpn-- <1036626+jpn--@users.noreply.github.com>

    ---------

    Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
    Co-authored-by: jpn-- <1036626+jpn--@users.noreply.github.com>

commit aa58cc4
Author: David Hensle <51132108+dhensle@users.noreply.github.com>
Date:   Fri Jan 16 03:31:07 2026 +1100

    Fix for zones reopening in simulation-based constraint mechanism for work/school location choice (ActivitySim#1028)

    * addresses issue with zones reopening after being closed in shadow_pricing

    * addresses issue with zones reopening after being closed in shadow_pricing

    * adding shadow price regression values

    * updating change log

    ---------

    Co-authored-by: juangacosta <juan.acosta@rsginc.com>

commit 6266ce4
Author: David Hensle <51132108+dhensle@users.noreply.github.com>
Date:   Thu Jan 8 10:26:48 2026 -0800

    Index names consistently set to "alt" for alternatives files (ActivitySim#1018)

    * "alt" now used as index in all alternatives modules

    * formatting

    * minor commenting

    * using stable sorting for unit test

    * adding to change log

    * updating school escort bundle Alt to alt

    * typo

    * Revert "updating school escort bundle Alt to alt"

    This reverts commit 625f685.

    * regenerate pipeline

    ---------

    Co-authored-by: juangacosta <juan.acosta@rsginc.com>
    Co-authored-by: Jeffrey Newman <jeff@driftless.xyz>

commit 0811191
Author: Jeffrey Newman <jeff@driftless.xyz>
Date:   Thu Jan 8 11:11:43 2026 -0600

    Repair CDAP estimation (ActivitySim#1026)

    * fix error in CDAP estimation model construction

    * update tests for CDAP

    * fix the other test file

    * add to changes.md

    * note on possible fixes

Author: dhensle

activitysim/abm/models/joint_tour_frequency_composition.py

@@ -44,11 +44,9 @@ def joint_tour_frequency_composition(
             model_settings_file_name,
         )
 
-    # FIXME setting index as "alt" causes crash in estimation mode...
     alts = simulate.read_model_alts(
-        state, "joint_tour_frequency_composition_alternatives.csv", set_index=None
+        state, "joint_tour_frequency_composition_alternatives.csv", set_index="alt"
     )
-    alts.index = alts["alt"].values
 
     # - only interested in households with more than one cdap travel_active person and
     # - at least one non-preschooler

activitysim/abm/models/school_escorting.py

@@ -308,7 +308,7 @@ def create_school_escorting_bundles_table(choosers, tours, stage):
         bundles["chauf_id"],
     )
 
-    bundles["Alt"] = choosers["Alt"]
+    bundles["alt"] = choosers["alt"]
     bundles["Description"] = choosers["Description"]
 
     return bundles
@@ -412,11 +412,7 @@ def school_escorting(
 
     trace_hh_id = state.settings.trace_hh_id
 
-    # FIXME setting index as "Alt" causes crash in estimation mode...
-    # happens in joint_tour_frequency_composition too!
-    # alts = simulate.read_model_alts(state, model_settings.ALTS, set_index="Alt")
-    alts = simulate.read_model_alts(state, model_settings.ALTS, set_index=None)
-    alts.index = alts["Alt"].values
+    alts = simulate.read_model_alts(state, model_settings.ALTS, set_index="alt")
 
     choosers, participant_columns = determine_escorting_participants(
         households_merged, persons, model_settings
@@ -565,10 +561,10 @@ def school_escorting(
             )
 
         if stage_num >= 1:
-            choosers["Alt"] = choices
-            choosers = choosers.join(alts.set_index("Alt"), how="left", on="Alt")
+            choosers["alt"] = choices
+            choosers = choosers.join(alts, how="left", on="alt")
             bundles = create_school_escorting_bundles_table(
-                choosers[choosers["Alt"] > 1], tours, stage
+                choosers[choosers["alt"] > 1], tours, stage
             )
             escort_bundles.append(bundles)
 

activitysim/abm/tables/shadow_pricing.py

@@ -860,10 +860,20 @@ def update_shadow_prices(self, state):
                 sprice.replace([np.inf, -np.inf], 0, inplace=True)
 
                 # shadow prices are set to -999 if overassigned or 0 if the zone still has room for this segment
-                self.shadow_prices[segment] = np.where(
+                old_shadow_prices = self.shadow_prices[segment].values
+                new_shadow_prices = np.where(
                     (sprice <= 1 + percent_tolerance / 100), -999, 0
                 )
 
+                # the conditions above allow for zones to be reopened, but we want to prevent such behavior
+                new_shadow_prices = np.where(
+                    (old_shadow_prices == -999) & (new_shadow_prices != -999),
+                    old_shadow_prices,
+                    new_shadow_prices,
+                )
+
+                self.shadow_prices[segment] = new_shadow_prices
+
                 zonal_sample_rate = 1 - sprice
                 overpredicted_zones = self.shadow_prices[
                     self.shadow_prices[segment] == -999